Phylogenetic Comparative Methods on Phylogenetic Networks with Reticulations

The Laplace Motion in Phylogenetic Comparative Methods

The majority of current phylogenetic comparative methods assume that the stochastic evolutionary process is homogeneous over the phylogeny or offer relaxations of this in rather limited and usually parameter expensive ways. Here we make a preliminary investigation, by means of a numerical experiment, whether the Laplace motion process can offer an alternative approach. INTRODUCTION – PHYLOGENET...

Shedding light on the ‘dark side’ of phylogenetic comparative methods

Phylogenetic comparative methods are becoming increasingly popular for investigating evolutionary patterns and processes. However, these methods are not infallible - they suffer from biases and make assumptions like all other statistical methods.Unfortunately, although these limitations are generally well known in the phylogenetic comparative methods community, they are often inadequately asses...

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters

UNLABELLED Phylogenetic trees are widely used to display estimates of how groups of species are evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees are obtained for several datasets (e.g. for different genes), then their clusters are often contradicting. Consequently, the set of all cluste...

Trying on Phylogenetic Footprinting Methods

Phylogenetic diversity and biodiversity indices on phylogenetic networks.

In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species according to their contribution to overall phylogenetic diversity. However, in many cases evolution is not treelike and thus, phylogenetic networks have been develop...